Two boys snatched by their father from their Queens home two weeks ago were found dead yesterday – after the dad told police his sons were in a “safe place” where no one would find them, cops said.

Police found the bodies of Richard Short, 7, and his brother, John, 3, covered by a Green Bay Packers jacket in a cold sub-basement of a Manhattan commercial building, said Chief of Detectives William Allee.

Until last week, their father, Ronald, had managed the building at 36 W. 25th St.

The bodies had been shoved behind maintenance equipment, mops and pails and tangles of wires in a room accessible only through a small door, Allee said.

Their bodies had decomposed, but it appeared the oldest boy suffered a blow to his head, police sources said.

He had been bound, and three-quarters of his body was covered by a black plastic bag, the sources said. An autopsy report is expected today.

Ronald Short, 49, who is being held on a bench warrant, refuses to answer questions from cops. His wife, Jolanta, 38, was questioned last night but is considered to be a witness.

Police sources quoted relatives as saying that Short feared he would be arrested for fighting with his wife, and “I’ll never see the kids again and I don’t want her to have them.”

Cops said the father had scratches on his legs but they didn’t know how recent they were.

Both the Queens and Manhattan DAs are investigating, because it’s not yet clear where the kids were killed.

Police had been hunting for the brothers since Jan. 13, when Jolanta told them her husband swiped their sons after a fight four days earlier in their Long Island City condo.

The family recently moved from Manhattan to the high-rise building at 4-74 48th Ave. overlooking the city, cops said.

Short allegedly hit his wife during the fight and she fled downstairs to a friend’s home, she said.

He grabbed his sons in a rage and left, she said.

Later, Short refused to tell his wife where their children were, saying they were “safe and sound” with relatives, Allee said. She frantically called family members, but no one knew where the children were.

Police concentrated their search on five Manhattan buildings Short managed for Rexton Realty Co. but found nothing.

Short was arrested Jan. 15 on two counts of endangering the welfare of a minor when he returned to the apartment.

He would not tell cops where to find his children, saying only that they were in a “safe place” and “no one will find them,” police sources said.

Short also told police he had paid someone $10,000 to watch the boys, sources said.

At the time, police said they did not suspect the children had been harmed.

Jolanta bailed her husband out of jail on Tuesday, and he was scheduled to appear in Queens Supreme Court on Thursday.

But he skipped the court appearance and was arrested on a warrant early Friday morning after showing up at St. Vincent’s Hospital in Manhattan claiming to be suicidal, police sources said.

Short hired a lawyer and would not cooperate in the hunt for his children, Allee said.

Police renewed their search, revisiting buildings managed by Short. He quit the job with Rexton last week, a company official told The Post.

The couple has a history of domestic disputes. In May, police were called to their Hudson Street home in Manhattan after Short allegedly pulled a knife on his wife, but she refused to press charges.